Recent genome-wide association studies (GWAS) and whole genome sequencing (WGS) have been successful in identifying novel Alzheimer's disease (AD)-associated risk genes and their functional variants, respectively. Our recent large-scale WGS efforts (Alzheimer's Genome Project, AGP-WGS; N = 1510 samples) have identified dozens of functional genetic variants that tightly co-segregate with familial AD. AD risk genes and their functional variants carry significant potential for unraveling the pathogenic mechanisms underlying AD, as well as provide new drug targets for the prevention and treatment of AD. The major challenge is to now fully characterize the pathogenic effects of AD-linked functional variants. To date, the field has lacked a single disease model system that fully recapitulates the pathogenic cascade of AD in a human neural system. In preliminary studies, we describe the creation of a novel human stem cell-derived 3D neural cell culture model in which familial AD mutations in the amyloid-? precursor protein (APP) and presenilin 1 (PSEN1) that induce extracellular ?-amyloid accumulation, also leads to neurofibrillary tangles. Thus, using this unique model system, we show for the first time that ?-amyloid deposition is sufficient to induce robust tauopathy, including hyperphosphorylated tau and detergent-resistant, silver-positive neurofibrillary tangles in a human neural cell system. No mouse model has previously achieved this without co-expressing both A?- and tau-related gene mutations. We now propose the following aims to employ our novel 3D human neural cell culture model to comprehensively assess novel AD genes and their functional variants for effects on AD pathogenesis. In Aim 1, we will investigate the impact of AD-risk genes and their functional genetic variants, identified b AGP-WGS, on ?-amyloid and tau pathologies, using our unique human 3D neural cell model system. In Aim 2, we will explore changes in gene expression and proteomic profile induced by excess ?-amyloid deposition in the human 3D neural cell model system. Potential interactions between AD risk genes/functional variants and molecular pathways triggered by excess ?-amyloid will also be explored. The overarching goal of the proposed studies is to construct a framework for systematically identifying and characterizing GWAS/WGS AD risk genes and their functional variants using our novel human 3D neural cell culture technology. Our studies should not only enhance our understanding of the etiology and pathology of AD, but also facilitate the discovery of novel AD drug targets for the treatment and prevention of AD.